crossing96/oncoscreening huggingface dataset:
EORTC risk tables are more suitable for Chinese patients with nonmuscle-invasive bladder cancer than AUA risk stratification.	BACKGROUND: Patients with non-muscle-invasive bladder cancer (NMIBC) need accurate estimations of the risk of recurrence and progression. Physicians can offer individualized therapy after identifying high-risk tumors. In our study, we compared the applicability of European Organization for Research and Treatment of Cancer (EORTC) risk tables and American Urological Association (AUA) risk stratification in Chinese patients with NMIBC. METHODS: We retrospectively studied 301 patients with NMIBC who underwent transurethral resection of bladder tumor (TURBT) between October 2000 and July 2009 at Huashan Hospital of Fudan University and analyzed their parameters. The recurrence and progression rates at 1 and 5 years postoperatively were calculated along with 95% confidence intervals. We compared them with results obtained from the EORTC risk tables and AUA risk stratification. P values <.05 were considered statistically significant. RESULTS: The median patient age was 67 years (21-92 years) and the median follow-up duration was 46 months (2-151 months). We used EORTC risk tables to classify patients into 3 groups, depending on whether they suffered recurrence or progression after TURBT. Kaplan-Meier curves showed significant differences among the 3 recurrence-free survival (RFS) levels (P < .0001, log-rank test) and among the 3 progression-free survival (PFS) levels (P < .0001, log-rank test). AUA risk stratification showed the same results. Both classifications were suitable to predict recurrence and progression in Chinese patients. However, for high-risk patients in both series, Kaplan-Meier curves showed significant differences between RFS levels (P < .0001, log-rank test) and between PFS levels (P < .0001, log-rank test). EORTC risk tables were stricter and AUA was more sensitive in assigning patients to a high-risk group. CONCLUSION: EORTC risk tables are better than AUA risk stratification for predicting recurrence and progression in Chinese patients with NMIBC, especially among high-risk patients.	bladder
"Background and Update for S1602 ""A Phase III Randomized Trial to Evaluate the Influence of BCG Strain Differences and T Cell Priming with Intradermal BCG Before Intravesical Therapy for BCG-naïve High-grade Non-muscle-invasive Bladder Cancer."	The S1602 Intergroup trial is a randomized phase III clinical trial that aims to test two important hypotheses: (1) priming with intradermal bacillus Calmette-Guérin (BCG) vaccine prior to standard intravesical BCG improves response to BCG in terms of recurrence-free survival and (2) Tokyo-172 BCG strain is non-inferior to TICE BCG in terms of time to high-grade recurrence. The study was approved by the Cancer Therapy Evaluation Program of the National Cancer Institute and activated in spring 2017. Here, we provide a synopsis of the study background, design, and update of the clinical trial.	bladder
Association between vascular endothelial growth factor rs699947 polymorphism and the risk of three major urologic neoplasms (bladder cancer, prostate cancer, and renal cell carcinoma): A meta-analysis involving 11,204 subjects.	BACKGROUND: The relationship between vascular endothelial growth factor (VEGF) gene variant rs699947 polymorphism and urologic neoplasms risk was studied extensively in recent years. The VEGF gene plays a key role in angiogenesis of urologic neoplasms, but some conclusions are still inconclusive. The aim of this study was to determine whether this polymorphism is a risk factor for susceptibility to urologic neoplasms by conducting a meta-analysis. METHODS: We performed a meta-analysis of 15 different publications from the PubMed, Embase and Medline databases, to better assess the association between VEGF rs699947 polymorphism and urologic neoplasms risk. Odds ratios (ORs) and 95% confidence intervals (CIs) were evaluated using random or fixed effects models. RESULTS: By pooling all eligible studies, we found that the VEGF rs699947 polymorphism was not associated with overall urologic neoplasms. However, subgroup analysis based on cancer types demonstrated that significantly increased association was found between VEGF rs699947 polymorphism and the risk of bladder cancer (BCa) under heterozygous genetic model (OR = 1.48, 95%CI = 1.17-1.89). And rs699947 polymorphism was also identified an increased risk of renal cell carcinoma (RCC) under dominant, recessive, homozygous, heterozygous and allelic contrast genetic models, while no association was observed in prostate cancer (PCa). In addition, in subgroup analysis by ethnicity, we found rs699947 polymorphism was associated with Asian population under dominant, homozygous, heterozygous and allelic contrast genetic models. No evidence of publication bias was found (Begg's test, P = 0.855; Egger's test, P = 0.590). CONCLUSIONS: In summary, our study showed evidence that the VEGF rs699947 polymorphism was obviously associated with an increased risk of bladder cancer and renal cell carcinoma, particularly in Asian population, while no significant association was observed in overall urologic neoplasms. Future studies with larger sample sizes are warranted to further evaluate these associations in more details.	bladder
Antimicrobial prophylaxis for transurethral resection of bladder tumor: A retrospective comparison of preoperative single-dose administration of piperacillin and tazobactam/piperacillin.	We aimed to clarify prophylactic antimicrobial effects of single-dose piperacillin (PIPC) for perioperative infections in the transurethral resection of bladder tumor (TURBT) in comparison with those of single-dose tazobactam/piperacillin (TAZ/PIPC) through a retrospective analysis. We analyzed data from 192 TURBT patients treated with single-dose (4 g) intravenous PIPC (P group) between April 2015 and April 2017. For comparison, we analyzed data from 50 TURBT patients treated with single-dose (4.5 g) intravenous TAZ/PIPC (T/P group) between June 2013 and April 2014. We compared the perioperative incidences of fever (≥38 °C) and bacteriuria in the two groups. The number of febrile patients was four (2.1%) in the P group and one (2.0%) in the T/P group, without significant difference (p = 0.970). Among these febrile patients, urine and blood samples of two patients in the P group tested positive for bacterial cultures of Citrobacter koseri and Enterococcus faecalis, respectively. None of the patients in the T/P group tested positive for urine culture, postoperatively. However, 22 patients (18.2%) in the P group tested positive for urine culture, and Staphylococcus epidermidis (six patients), E. faecalis (three patients), Escherichia coli (three patients), Streptococcus agalactiae (two patients), Staphylococcus aureus (two patients), and C. koseri (one patient) were isolated. There was no significant difference in the incidence of bacteriuria in these two groups (p = 0.055). Based on these results, single-dose PIPC administration for the prevention of perioperative infections in TURBT was as effective as TAZ/PIPC.	bladder
Efficacy of intra-arterial chemotherapy combined with intravesical chemotherapy in T1G3 bladder cancer when compared with intravesical chemotherapy alone after bladder-sparing surgery: a retrospective study.	PURPOSE: To assess the efficacy of intra-arterial chemotherapy (IAC) combined with intravesical chemotherapy (IVC) in T1G3 bladder cancer (Bca) after transurethral resection of bladder tumor (TURBT). METHODS: Our study retrospectively reviewed 200 patients with T1G3 BCa who had all undergone TURBT. The patients' medical records were divided into two groups, one group only had IVC with pirarubicin after surgery, and the other group had IAC (cisplatin and epirubicin) combined with IVC after surgery. The patients were monitored regularly by urine cytology and cystoscopy. Survival and recurrence curves were calculated using the Kaplan-Meier method. Tumor recurrence, progression and tumor-specific death rate were compared with Chi-square test. A multivariate analysis was carried out to find out potential confounders. RESULTS: A total of 200 medical record was analyzed, 131 patients received IVC, 69 IAC + IVC treatment, tumor-specific death rate between the combined IAC and IVC compared to IVC alone was 7.25 and 17.6%, respectively (p < 0.05); the tumor recurrence rate between the two groups was 31.8% (22/69) and 44.3%, respectively (58/131) (p < 0.05), and tumor recurred later in the IAC + IVC group (p < 0.05), tumor progression rate was 18.8% (13/69) and 28.2% (37/131), respectively, with p < 0.05. Overall survival was longer in IAC + IVC group (p < 0.05). Using the multivariable regression model, IAC was significantly related to disease recurrence (p < 0.05) and overall survival (p < 0.05). CONCLUSION: T1G3 BCa post-TURBT surgery patients who underwent IAC combined with IVC had a longer overall survival and increased time interval to first recurrence, lower tumor recurrence rate, progression rate and tumor-specific death rate than compared with those who only underwent IVC alone.	bladder
CC Chemokine Ligand 18 Promotes Cell Proliferation and Metastasis of Urothelial Carcinoma via Activating PI3K/mTOR Signaling in Patient with Renal Transplantation.	OBJECTIVE: The study aimed to investigate the role of chemokine (C-C motif) ligand 18 (CCL18) in the progression of urothelial carcinoma (UC) after renal transplants (RT). METHODS: Tissues were collected from 60 patients with UC in which 24 were after RT. The tissues were all obtained from patients after radical cystectomy. Expression levels of CCL18 were examined by immunohistochemistry, RT-polymerase chain -reaction (RT-PCR), and quantitative RT-PCR, respectively. WST-1 assay was performed to determine proliferative capacity of UC cells. Migration and invasion of UC cells were analyzed by the using of chemotaxis and Transwell system. Western blotting was applied to assess the activation of PI3K-mTOR (Mammalian Target of Rapamycin) signaling. RESULTS: Compared to normal urothelial tissues, the expression levels of CCL18 were significantly increased in tumors of UC, and even more in tumors of UC after RT. Ectopic expression of CCL18 efficiently enhanced the proliferation of UC cells and moreover, exacerbated the migration and invasion of UC cells. Furthermore, overexpressed CCL18 increased the phosphorylation of PI3K, Akt, and mTOR in UC cells, suggesting the hyperactivation of PI3K/Akt/mTOR signaling. CONCLUSIONS: The results demonstrate the critical role of CCL18 in the progression of UC, especially in receipt with RT. Our study indicates that CCL18 could serve as a biomarker and therapeutic target in diagnosis of recipients with UC after RT.	bladder
[Palliative surgery for metastatic urothelial cancer].	Palliative surgery is performed in order to relieve symptoms as well as to increase survival in selected tumour entities. For urothelial cancer, its role is limited and clinical data are limited, too. Yet with better responses being achieved to systemic therapy, more and more surgical procedures are being carried out in the form of individualised treatment concepts and are then published as case series. For patients with low metastatic load, or if the tumour is restricted to lymph nodes inside and outside the pelvis, as well as for singular pulmonary metastasis, there seems to be a survival benefit in select cases. Calculation of risks and benefits is difficult and, for now, should be reconsidered for every individual patient. Therefore, prospective trials are difficult to perform and should not be expected to exist in the future. This review aims to summarise the most important publications on this topic.	bladder
Diagnostic and prognostic biomarkers of common urological cancers based on aberrant DNA methylation.	AIM: We intended to construct DNA methylation-based models for the diagnosis and prognosis of three common urological cancers including prostate adenocarcinoma, renal clear cell carcinoma and bladder urothelial carcinoma. MATERIALS & METHODS: Total 450K methylation array data from the cancer genome atlas and gene expression omnibus datasets were downloaded. Moderated t-statistics and least absolute shrinkage and selection operator method were used to build diagnosis and prognosis models. RESULTS: Our diagnostic panels including 128 CpG sites had high sensitivity and accuracy in distinguishing samples and could identify lymphatic metastases in prostate adenocarcinoma patients. The prognostic models with 19 CpG sites for renal clear cell carcinoma and 21 CpG sites for bladder urothelial carcinoma were able to distinguish high- and low-risk patients and improve the predictive ability of the tumor node metastasis staging system. CONCLUSION: DNA methylation may afford reliable biomarkers in the diagnosis and prognosis of common urological cancers.	bladder
Beyond first-line systemic treatment for metastatic urothelial carcinoma of the bladder.	Metastatic urothelial carcinoma of the bladder is a rarely curable disease. Patients receive systemic therapy with limited response rates and survival benefits. The rescue regimens of these patients who have failed first-line treatment had remained problematic until the recent advances. Several trials with novel regimens, including immune checkpoint inhibitors and targeted therapy, to salvage relapsed urothelial carcinoma of the bladder have recently been published. However, the choice of an optimal treatment regimen remains challenging in the absence of randomized trials comparing regimen sequences. Daily clinical cases provoke the question of whether there is a preferred second-line regimen. This paper provides an overview of recent trials and proposes a management algorithm based on subgroup analyses and prognostic features.	bladder
Validation of a High-End Virtual Reality Simulator for Training Transurethral Resection of Bladder Tumors.	"OBJECTIVE: The oncological outcome in patients with bladder cancer (BC) significantly correlates with the quality of transurethral resection of bladder tumors (TUR-BT). Virtual reality (VR) training simulators have been developed to improve surgical skills. We evaluated the advantages and limitations of the novel Uro Trainer (UT) (Karl Storz GmbH, Germany) with respect to training for TUR-BT. DESIGN: Participants underwent VR training based on 4 different TUR-BT cases accompanied by self-assessment and evaluation questionnaires. Results were compared between experienced endourologists and novices, and furthermore, correlated with self-rated capabilities for content and construct validity. Student's t tests, Pearson's correlation, and chi-squared tests were performed for statistical evaluation. SETTING: The study was performed at the tertiary care urological department of the Ludwig-Maximilians-University, Munich, Germany. PARTICIPANTS: A total of 22 urological physicians, including residents and consultants, were included in the study. RESULTS: There is a need to improve TUR-BT training as 27.3% of the participants had already experienced overtaxing situations during TUR-BT and only a few reported of high satisfaction with the classical ""see one-do one"" teaching mode. Construct validity was demonstrated, as consultants achieved significantly higher overall scores (p < 0.001) and safety (p = 0.004) and visualization (p = 0.001) subscores. Interestingly, the self-assessed capability to perform a TUR-BT correlated significantly (p = 0.01) with overall UT scores. Significant progress of self-rated abilities was shown for several parameters, including inspection (p = 0.046) and resection (p = 0.026). Although participants indicated improvements in several procedural skills and overall benefit of the VR training with the UT was rated 4.6 on a 5-point scale by consultants, limitations of the UT were demonstrated predominantly for tissue feedback and authenticity of different tissue layers. CONCLUSIONS: The novel VR simulator showed a high face and construct validity, and therefore has a great potential to complement endourological training."	bladder
LncRNA CALML3-AS1 promotes tumorigenesis of bladder cancer via regulating ZBTB2 by suppression of microRNA-4316.	An increasing number of studies have elucidated the essential roles of long noncoding RNAs (lncRNAs) in tumor development. LncRNAs are also closely associated with bladder cancer (BCa) progression. In the present study, we screened out a novel lncRNA CALML3-AS1 with increased expression value in BCa tissues. Particularly, we showed that CALML3-AS1 overexpression correlates with advanced staging and an unsatisfactory prognosis. Functional experiments illustrated that CALML3-AS1 knockdown suppressed BCa cell proliferation, arrested cell-cycle progression and impaired migration and invasion while promoting apoptosis. Mechanistic investigation revealed that CALML3-AS1 directly interacts with miR-4316 and inhibits its availability in BCa cells, leading to elevated expression of ZBTB2. Consequently, ZBTB2 promotes BCa tumorigenesis through repressing p21 and facilitating PDK4 transcription. In conclusion, our findings demonstrate a novel CALML3-AS1-mediated process involved in BCa progression and indicate it might be a promising therapeutic target.	bladder
Genomic case report of a low grade bladder tumor metastasis to lung.	BACKGROUND: We present a rare case where distant metastasis of a low grade bladder tumor was observed. We carried out detailed genomic analysis and cell based experiments on patient tumor samples to study tumor evolution, possible cause of disease and provide personalized treatment strategies. CASE PRESENTATION: A man with a smoking history was diagnosed with a low-grade urothelial carcinoma of the bladder and a concurrent high-grade upper urinary tract tumor. Seven years later he had a lung metastasis. We carried out exome sequencing on all the patient's tumors and peripheral blood (germline) to identify somatic variants. We constructed a phylogenetic tree to capture how the tumors are related and to identify somatic changes important for metastasis. Although distant metastasis of low-grade bladder tumor is rare, the somatic variants in the tumors and the phylogenetic tree showed that the metastasized tumor had a mutational profile most similar to the low grade urothelial carcinoma. The primary and the metastatic tumors shared several important mutations, including in the KMT2D and the RXRA genes. The metastatic tumor also had an activating MTOR mutation, which may be important for tumor metastasis. We developed a mutational signature to understand the biologic processes responsible for tumor development. The mutational signature suggests that the tumor mutations are associated with tobacco carcinogen exposure, which is concordant with the patient's smoking history. We cultured cells from the lung metastasis to examine proliferation and signaling mechanisms in response to treatment. The mTOR inhibitor Everolimus inhibited downstream mTOR signaling and induced cytotoxicity in the metastatic tumor cells. CONCLUSION: We used genomic analysis to examine a rare case of low grade bladder tumor metastasis to distant organ (lung). Our analysis also revealed exposure to carcinogens found is tobacco as a possible cause in tumor development. We further validated that the patient might benefit from mTOR inhibition as a potential salvage therapy in an adjuvant or recurrent disease setting.	bladder
New method to preserve the original proportion and integrity of urinary cell-free DNA.	BACKGROUND: Due to high nuclease activity and complex contents in urine, urinary cell-free DNA (ucfDNA) was prone to degrade. So, we developed standardized urine collection tube (UCT) to prevent ucfDNA degradation and simultaneously maintain urinary cells in their original form during the sample collection process, ensuring stabilization of the original proportion and integrity of ucfDNA. METHODS: Urine samples were collected from bladder cancer patients and divided into 10-mL normal tubes and 10-mL UCTs, respectively, and kept at ambient temperature. Urine supernatant was separated by centrifuging, and ucfDNA was extracted. Then ucfDNA was quantified by quantitative real-time polymerase chain reaction. UcfDNA fragments distribution was analyzed by Agilent 2200, and the frequency of specific mutations of urinary system disease was detected by next-generation sequencing method. RESULTS: Urine collected into UCTs showed no statistically significant changes in their original proportion and integrity of ucfDNA up to 7 days at ambient temperature and also ucfDNA fragments were maintained well. Conversely, urine collected into normal tubes was observed an obviously decline in their original proportion of ucfDNA and ucfDNA fragments changed greatly. The △% of allele fraction (AF) for specific genes of ucfDNA from UCTs was lower than from normal tubes by 3.7-fold. CONCLUSION: Using UCTs, they can maximally keep the original proportion and integrity of ucfDNA and stabilize urinary cells and minimize the background noise caused by urinary cellular DNA releasing, it will be help to open the door of next-generation noninvasive liquid biopsy applications utilizing urine.	bladder
The molecular limitations of biomarker research in bladder cancer.	PURPOSE: Urothelial carcinoma of the bladder (UCB) is a common malignancy with limited systemic treatment options in advanced stages. Despite recent advances in immunotherapy, the majority of patients do not respond to these treatments. There is an unmet need for developing robust biomarkers to inform treatment decisions and identify patients who are likely to respond. METHODS: A MEDLINE/PubMed literature search was performed, focusing on tissue-based and circulating biomarkers, and their potential in muscle-invasive UCB. RESULTS: UCB is a heterogeneous disease that consists of several clonal and subclonal populations, each with a mix of truncal and private genomic alterations. This inter- and intra-tumoral heterogeneous landscape results in the development of treatment resistance. Tumor heterogeneity also constitutes a barrier to the development of robust markers of response and resistance to chemotherapy and immunotherapy. Defects in DNA repair genes and a high tumor mutational burden independently confer sensitivity to cisplatin-based chemotherapy and checkpoint inhibitors. Oncogenic alterations such as FGFR3 mutations and fusions are associated with response to FGFR3 inhibitors. Several emerging potential biomarkers, including gene expression-based molecular subtypes, T-cell receptor clonality, and tissue- or blood-based immune-gene profiling, require prospective testing and validation. Tissue-based biomarkers such as PD-L1 immunohistochemistry have several limitations due to discordance in assay methodology and trial designs. Novel liquid-biopsy techniques are promising as potential biomarkers. CONCLUSIONS: Validated biomarkers that capture the complexity of the biology of both the tumor and the tumor microenvironment are needed in muscle-invasive UCB. Standardization of methods is critical to developing reliable biomarkers to guide clinical management.	bladder